Chaco Canyon, Its World, and Ours

A few years ago I did a series of posts called “Aftermath” that consisted of short commentaries on the chapters in The Prehistoric Pueblo World, a volume edited by Michael Adler that synthesized information on the archaeology of the Pueblo III period (AD 1150 to 1350) in various regions of the Southwest. This period postdated the decline of Chaco Canyon as a major regional center, and understanding it is important for understanding the relationship between Chaco and the modern Pueblos, as well as for understanding some aspects of Chaco itself.

Another period that is of perhaps even greater interest for understanding Chaco is the Pueblo I period (generally defined as AD 750 to 900, but see below), which immediately predates Chaco’s rise to regional dominance. I was therefore pleased to see the publication in 2o12 of Crucible of Pueblos: The Early Pueblo Period in the Northern Southwest, a volume synthesizing information on the Pueblo I period along the same lines as Adler’s effort for Pueblo III. It’s edited by Rich Wilshusen, Gregson Schachner, and James Allison, all of whom have made important recent contributions to understanding of this under-researched period. I’m just now getting around to reading it, and I decided to do a similar series of posts commenting on the chapters as I read them. I’m entitling the series “Foreshadow” to indicate the way developments during this period seem to, well, foreshadow later developments at and involving Chaco.

This post addresses the introduction, which is by the three editors of the volume along with Kellam Throgmorton, who is not otherwise a familiar name (at least to me) but who is thanked in the acknowledgments for his work “reimagining” this chapter. He was apparently a graduate student at the University of Colorado at the time, and has since graduated and is now “doing contract archaeology work in New Mexico.” The introduction as it stands is very engaging and readable, so if that was Throgmorton’s doing I can see why the volume editors took care to thank him specifically.

This introductory chapter is primarily a history of archaeological research on the Pueblo I period in the Southwest, but it also situates that history in the context of archaeological understanding of that period and how it relates to others, which has changed markedly over time. It also explains the reasoning for this volume’s use of “Early Pueblo” rather than “Pueblo I” to describe the period of interest, which is defined more broadly than Pueblo I has traditionally been. As with so much else in Southwestern archaeology, the issues here go back to the classification developed at the first Pecos Conference in 1927. As this chapter makes clear, this was initially primarily a developmental sequence rather than a chronological one, and the Pueblo I period in particular has been misunderstood on this account. This volume therefore uses a more general “Early Pueblo” period of circa AD 650 to 950 to frame the developments in the regions it discusses, which covers the various definitions that have been used for Pueblo I in different areas, as well as parts of Basketmaker III in some because of the importance of immediately preceding events for understanding Pueblo I.

The bulk of this chapter relates the history of understanding of the Pueblo I period by archaeologists. This history follows the familiar sequence of culture history/classification followed by processualism/environmental determinism followed by post-processualism/neohistoricism, but with an emphasis on how the Pueblo I period tended to be subsumed by larger theoretical constructs until the rise of large cultural resource management projects in the 1970s and 1980s massively increased the data available and forced a reevaluation of the period. The most influential of these efforts was the Dolores Project, which happened to occur in an area that was one of the most important centers of Pueblo I village development. The massive scale of this project, the largest ever in the US at the time, led to a much more detailed understanding of the Pueblo I period and the recognition that, rather than a brief interlude in the sequence of development from small hamlets to large pueblos, this was a time of rapid formation of the first major agricultural villages in the northern Southwest, followed by their equally rapid dissolution and a massive outmigration of people from the region. The precision of tree-ring dating allowed for very fine-grained understanding of the chronology, and the results of the project showed a level of dynamism in population movement and culture change that was totally unexpected and hard to fit in the gradual progression paradigm underlying the traditional Pecos classification.

Furthermore, certain aspects of the short-lived Dolores villages were strikingly reminiscent of the well-known Chacoan communities that emerged to the south shortly afterward, which led to the increasingly accepted idea that the formation and dissolution of villages during Pueblo I in the Dolores area were events that directly influenced the rise of Chaco. Indeed, it is now considered quite likely that many of the people who were involved in the development of early great houses at Chaco had moved there from Dolores.

So that’s the main message in this chapter, which also serves as an introduction to the volume itself and the other chapters in it. The next few chapters cover the specifics of settlement patterns in several parts of the northern Southwest, including not just the Mesa Verde region (the focus of most Pueblo I research so far) but also Chaco and its surroundings as well as areas further south and east. The latter two areas are often not addressed very well in research on this period, so I’m very interested in seeing the information on them presented here. The next few chapters cover a few broad thematic issues of interest for understanding this period across all the regions, then there are concluding chapters by Steve Lekson and John Kantner putting all this in a larger perspective. Overall this seems like a well-designed and desperately needed synthesis of an important but poorly understood period in Southwestern prehistory, and I’m eager to dive into the details.

Unmanned aerial vehicles (UAVs), popularly known as “drones,” have become increasingly common in recent years as the technology behind them has developed. Some uses are controversial, such as military applications and uses that might violate privacy expectations or be dangerous to other aircraft, but other uses are more benign and can potentially open up new frontiers.

In archaeology, UAVs are increasingly being used for aerial photography and remote sensing in many places around the world. These are types of research that have been established for decades, but that until recently were prohibitively expensive for most archaeologists since they required both expensive camera equipment and the use of airplanes or helicopters. With the development of both lighter, less expensive cameras and UAVs that are robust enough to carry them, this type of research is now much more practical.

Blue J is in an area at the southern edge of the San Juan Basin that is thick with Chacoan outlier communities, most of which date to fairly early in the Chacoan era and many of which were apparently abandoned while the Chaco system was flourishing. Casamero Pueblo is one site very close to Blue J where a great house has been excavated and is open to public visitation. These communities typically have one or more great houses and great kivas, and in fact it is unusually common for communities here to have multiple great houses compared to other Chacoan outlier communities. At Blue J, however, Kantner has so far not identified any great houses or great kivas. As he says on his website:

Turquoise, marine shell, jet, azurite, malachite, and other exotic materials attest to the success of Blue J’s inhabitants. Oddly, however, what was originally thought to be a great house turned out to be a normal residential structure, making Blue J the only community for miles around without Chacoan architectural influence.

Now, part of what’s going on here may have to do more with how archaeologists define “great house” than with anything about Blue J specifically. The function of the monumental buildings that have been given this label remains a point of active contention among scholars, with some arguing that they were primarily residential, perhaps housing community elites or religious leaders, and others arguing that they were non-residential public architecture, perhaps with ritual significance as sites of pilgrimage and/or communal feasting. Kantner belongs to the latter camp, so finding “normal” residential features at a suspected great house removes it from consideration as such, whereas another archaeologist might interpret such findings differently. (It’s worth noting that many if not most excavated “great houses” have showed at least some evidence for residential use, and in some cases they have not been noticeably different from other residential structures in a community except in size and location.)

The focus of the recent study was on demonstrating the potential for using UAVs to do fast, inexpensive survey of large sites and to identify buried features. Blue J is well suited for this on both counts. It is located at the foot of a steep cliff, which has resulted in many sites in the community being covered with substantial deposits of sediment carried by water and wind, making them difficult to identify on the surface. It is also fairly large for a Chacoan outlier community, with over 50 residential sites identified through previous surveys, which makes a fast method of survey over a large area an attractive proposition.

The study consisted of doing several flights with a UAV over the site, at different times of day and night, primarily with the infrared thermal camera to capture differences in temperature that are expected to be present between archaeological features and the dry desert soil. The original intent was to do some of the flights in the hottest part of the afternoon, but high winds ended up making this impossible. The results were nevertheless impressive: one site that had been previously identified through survey and limited excavation showed up clearly in the imagery, with buried walls visible in some of the images. Several other sites that had been identified but not excavated showed up as well, with buried walls again visible. A large circle showing a possible great kiva is particularly interesting given that no great kiva has yet been identified from surface survey.

Obviously further work is necessary to confirm some of the results from the imaging, but this is a very successful demonstration of the potential for this technology to improve survey and site identification so that further research can be focused on the most promising locations for sites. Other sensing techniques such as ground-penetrating radar have also been tried in the Southwest, but they are much slower and can be thrown off by some characteristics of the desert environment. Aerial thermography using UAVs offers another option that seems to have a lot of potential and it will be interesting to see how it is used as the technology continues to advance.Casana, J., Kantner, J., Wiewel, A., & Cothren, J. (2014). Archaeological aerial thermography: a case study at the Chaco-era Blue J community, New Mexico Journal of Archaeological Science, 45, 207-219 DOI: 10.1016/j.jas.2014.02.015

Today is the winter solstice, which means it’s also the sixth anniversary of this blog. On these anniversaries I like to write about archaeoastronomy, which is a very interesting topic and an important one for understanding Chaco and Southwestern prehistory in general. Last year I wrote about some research indicating that in the Rio Grande valley, an area generally thought to be outside the Chaco system but that was certainly occupied at the same time as Chaco, there was a long and very consistent tradition of orienting pit structures to the east-southeast, which is the direction of winter solstice sunrise. The winter solstice is very important in the cosmology and rituals of the modern Pueblos, so it makes a lot of sense that at least some Pueblo groups would orient their dwellings based on it.

As I noted at the time, this orientation is very different from that in the San Juan region to the west, including Chaco and Mesa Verde. In this area there is an equally long tradition of orienting pit structures to either due south or south-southeast. I’ve long wondered why this might be, and an article I read recently discusses the issue and proposes some interesting potential answers.

The article is by Kim Malville and Andrew Munro and was published in the journal Archaeoastronomy in 2010 as part of a special issue on archaeoastronomy in the Southwest. Malville is an astronomer who has done a lot of research on archaeoastronomy in the Southwest and identified many potential astronomical alignments, but this article is actually largely about debunking many of the alleged alignments claimed by others, particularly Anna Sofaer and her Solstice Project. Sofaer, an artist who turned her attention to archaeoastronomy after discovering the “Sun Dagger” effect involving a spiral petroglyph on Fajada Butte that on the summer solstice appears (or appeared) to be bisected by a “dagger” of light coming through a slit between large boulders in front of it. Sofaer went on to organize surveys of the major great house sites in Chaco Canyon to identify any celestial alignments in the orientation of their walls, and her team found that virtually all of them did show alignments to the positions of the sun or moon on solstices, equinoxes, or lunar standstills.

Light Snowfall on Fajada Butte

Sofaer and her collaborators went on to publish these findings widely, and to make a well-known documentary that has often been shown on television and inspired a lot of interest in Chaco. As Malville and Munro show in this paper, however, the evidence for these alignments is very thin. There is little to no justification in Pueblo ethnography for the idea of celestial building alignments, and the alignments themselves are identified with a substantial margin for error that makes spurious positive identifications likely, especially when so many potential alignments are tested for. Particularly concerning is how many of the alignments are to the minor lunar standstill, which is not a very impressive or noticeable event. (The major lunar standstill is a different story, and there is strong evidence at Chimney Rock in Colorado that the Chacoans were familiar with it and considered it important.) Malville and Munro also argue that the fact that most of the alignments are based on the rear walls of sites is also questionable, since there is no evidence that rear wall alignments were or are important culturally to Puebloans.

Instead, they argue that the alignments of rear walls are epiphenomenal, and that they mostly result from the more solidly established concern with the orientation of the front of a site. The bulk of the article is devoting to tracing these frontal orientations across time and space, with a primary focus on Chaco itself and on the earlier Pueblo I villages in the area of Dolores, Colorado that are often seen as being partly ancestral to the Chaco system.

As I noted above, there are two main orientations that persist through time in the San Juan region. One is to due south, and the other is to the south-southeast (SSE). With pit structures these axes are typically defined by a straight line of sipapu (if present), hearth, deflector, and vent shaft. There is often also a measure of bilateral symmetry between features on either side of this line, such as support posts. When there are surface rooms behind a pit structure, they often (but not always) conform to the same alignment, and when the back of a row of surface rooms is straight, it is typically perpendicular to the main orientation. Malville and Munro argue that these perpendicular back walls on many Chacoan great houses, which Sofaer has identified as having alignments to various astronomical phenomena, are really subsidiary effects of the main emphasis on frontal orientation.

The authors start their survey of orientations with the Basketmaker III pithouse village of Shabik’eschee at Chaco. Of 15 pithouses for which they could find adequate information on orientation, 11 faced SSE with an average azimuth of 153.7 degrees and 4 faced south with an average azimuth of 185 degrees. Strikingly, none of the pithouses showed any other orientation.

The north-south orientation isn’t difficult to understand, and Malville and Munro attribute it to use of the night sky for navigation (which would have been easy enough at this time even though there wasn’t actually a north star), and they also mention the widespread presence of Pueblo traditions mentioning origins in the north. While the exact reasons for adoption of this orientation may not be clear, its consistency isn’t unexpected since it’s pretty obvious and easy to replicate.

The SSE orientation, on the other hand, is a different matter. Note that at Shabik’eschee this was much more common than the southern orientation, from which it is offset by about 20 to 30 degrees in individual cases. There is more variation in this orientation than with the southern one (standard deviation of 7.7 degrees versus 2.4), but it’s sufficiently consistent and common that it seems like there must be some specific reason for it. Unlike the southern orientation, however, it’s not at all clear what that might be. Malville and Munro, sticking to their interpretation of orientations as references to places of origin, suggest that in the case of Shabik’eschee it might reflect the fact that some people might have migrated to Chaco from an area that was more to the north-northwest than due north, which seems implausible to me but then I don’t have a better explanation myself.

McPhee Reservoir, Dolores, Colorado

In any case, this pattern continues through time. The next set of orientations Malville and Munro look at are those of the pit structures at the Pueblo I Dolores villages. What they find is that SSE orientations are dominant here too, even more so than at Shabik’eschee. In fact, all of the pit structures they looked at had SSE orientations except those at Grass Mesa Village, which mostly faced faced south (although even here there were a few SSE orientations). This is in keeping with other evidence for differences in architecture among different villages at Dolores; Grass Mesa is known for having long, straight room blocks, as opposed to the smaller and often crescent-shaped roomblocks at McPhee Village, which with it is most often compared.

The Duckfoot site, to the west of the Dolores villages but contemporaneous with them, also had a SSE orientation. Further west, however, southern orientations become more common, including at the important village sites of Yellow Jacket and Alkali Ridge, plus some of the earlier Basketmaker II sites on Cedar Mesa in Utah.

There was one more orientation used during the Pueblo I period in the Northern San Juan region, however. At Sacred Ridge, in Ridges Basin near modern Durango, Colorado, the average azimuth of the pit structures is 120 degrees, the same east-southeast orientation corresponding to winter solstice sunrise so common in the Rio Grande. Malville and Munro remark on the similarity to the Rio Grande pattern and consider it “puzzling,” positing some potential ways that it could have come about. They argue, however, that wherever this pattern came from it didn’t last in the north, and they point to the extremely violent end to the occupation of Sacred Ridge as the end of this orientation tradition in the San Juan region (although this may not be strictly true, as discussed below).

From here Malville and Munro turn back to Chaco. Specifically, they look at the great houses at Chaco during its heyday from about AD 850 to 1150. Rather than pit structures, they focus on roomblocks, and they interpret the orientation of a roomblock to be the perpendicular to its long axis (in the case of rectangular roomblocks) or the perpendicular to the ends of the crescent of roomblocks with that shape. They find that most of the great houses have a SSE orientation, in keeping with the general trend throughout the region, as do the three northern outlier great houses of Chimney Rock, Salmon, and Aztec. Since this orientation is very close to the perpendicular of the minor lunar standstill moonrise alignment that Sofaer has proposed for many of these buildings, Malville and Munro argue that this widespread orientation explains the pattern much better than the lunar alignment. Pueblo Alto and Tsin Kletzin have north-south orientations, which is unsurprising since they lie on a north-south line with each other.

A few of the great houses have a more complicated situation. Peñasco Blanco appears to face east-southeast at an azimuth of approximately 115 degrees. This is intriguingly close to the Rio Grande/Sacred Ridge winter solstice orientation, which Malville and Munro do note. Although the unexcavated nature of the site makes it hard to tell for sure, it is possible that this is in fact an example of this orientation surviving much later in the San Juan region than the destruction of Sacred Ridge, although what, if any, connection there might be between the two sites is unclear.

Pueblo Bonito from Above

And then there’s Pueblo Bonito. While the very precise north-south and east-west cardinal alignments of some of the key walls at this site are well known, it has also long been noted that there is evidence for different alignments and change over time here. Malville and Munro interpret the early crescent shape of the building as having a SSE orientation, and like many others they relate it to the similar size, shape, and orientation of McPhee Pueblo at McPhee Village. They then describe multiple stages of drift away from this orientation toward the cardinal orientation. There is surely something to this interpretation, but a careful look at the stages of construction of the site shows that the picture is probably more complicated. The very first construction at Bonito appears to have been straight and oriented to the south, and to have been incorporated later into the SSE-facing crescent. Subsequent building stages show evidence of both orientations having been present throughout the history of the building.

The complicated situation at Pueblo Bonito provides a convenient segue to the key issue here: what was driving this long-term but consistent variation? Why were two different orientations for buildings present in close proximity for hundreds of years, even as populations moved long distances and adjusted their cultures in profound ways? Malville and Munro suggest that these orientations may reflect longstanding cultural and ethnic diversity in the prehistoric Southwest. Given how long-lived and consistent these patterns are, they propose that they were related to deep-seated cultural identities. This is an intriguing idea that may allow tracking of specific cultural groups across the Southwest over centuries. It also provides another piece of evidence that Chaco Canyon was a multicultural community, and implies that even Pueblo Bonito itself contained groups with diverse backgrounds.

The picture is probably even more complicated than Malville and Munro suggest. They tend to implicitly assume that the orientations of pit structures are the same as those of the room blocks with which they are associated, but at least at Chaco this is not necessary true, particularly for small-house sites, which they also don’t address at all in this study. There are many examples of small houses where the room blocks are oriented to the east but the pit structures are oriented to the south (and possibly also SSE, although I haven’t checked this). This eastern orientation may reflect connections to the south, which have gotten a lot less attention in the literature than connections to the north although they appear to have been pretty important in the origins of Chaco.

In any case, I think this is fascinating stuff. It may not be archaeoastronomy per se, but it seems like a fitting way to mark the solstice.Malville JM, & Munro AM (2010). Cultural Identity, Continuity, and Astronomy in Chaco Canyon Archaeoastronomy, 23, 62-81

Overall, the evidence from all these different sources is very consistent in indicating that the modern Pueblos of New Mexico and Arizona are clearly the descendant communities of the ancient Pueblos in a general sense, but that tracing a line of descent between any specific ancient site and any specific modern Pueblo is not currently possible. With further research, however, I think there is a lot of potential for identifying more specific connections using multiple lines of evidence.

Having introduced the basics of archaeological use of DNA evidence, and discussed some other applications of DNA studies in archaeology, let’s take a look at the data relevant to the Southwest specifically. For modern populations in North America overall, there are some broad trends that have been identified in mitochondrial haplogroup distribution by region, as first elucidated by Joseph Lorenz and David Glenn Smith of UC Davis in 1996. They only looked at haplogroups A, B, C, and D, since haplogroup X had not yet been identified as a founding haplogroup at that time. Their results showed that there are definite patterns in haplogroup distributions by region. For the Southwest specifically, they found most groups showed very high levels of B and low levels of A, despite the fact that A was the most common haplogroup in their sample overall. The main Southwestern groups that showed high levels of A were the Athabascan-speaking tribes (Navajo and Apache), which is unsurprising since northern Athabascan groups, along with most other groups in the Arctic and Subarctic, are almost exclusively A, and it’s well established that the southern Athabascans immigrated into the Southwest from the north relatively recently. Some other Southwestern groups show some representation of A as well, which Lorenz and Smith attribute to intermixing with the Athabascans (although as I’ll discuss below this doesn’t seem to be the whole story). Similarly, the Navajos and Apaches showed substantial representation of B and C, unlike their northern cousins, and this is probably due to intermixing with the Pueblos and other Southwestern populations.

A subsequent study by Smith, Lorenz, and some of their students at Davis looked specifically at haplogroup X, which had been identified in both modern and ancient Native American samples by then and was established as a founding haplogroup. They found it widely distributed among modern populations speaking a variety of languages but particularly among speakers of Algonquian and Kiowa-Tanoan languages. The Kiowa-Tanoan connection is of particular interest for Southwestern purposes, of course, as this is one of the main language families spoken by the eastern Pueblos in New Mexico. In this case, haplogroup X was found in the Kiowa and Jemez samples. This is very interesting since the Jemez are Pueblo and the Kiowa are not, and the relationship between the Kiowa and the Tanoan-speaking Pueblos is a longstanding mystery. It’s hard to know how to interpret the haplogroup X data in this connection. Since X is so rare overall the fact that it is so concentrated in certain groups seems meaningful somehow, but since it’s still pretty rare in those groups and little follow-up research on this has since been done it remains quite mysterious.

Turning to the ancient evidence, the first work in the Southwest was associated mostly with the University of Utah. In 1996 Ryan Parr, Shawn Carlyle, and Dennis O’Rourke published a paper reporting on aDNA research on the remains of 47 Fremont individuals from the Great Salt Lake area, 30 of which could be assigned to a haplogroup. The Fremont have always been something of a mystery, with many Southwestern cultural features but living on the northern fringes of the Southwest and having some notable differences from Pueblo cultures to the south. What the Utah researchers found, however, seemed to show the Fremont patterning genetically with the Pueblos rather than with other groups in the Great Basin or Plains. Haplogroup A was completely missing from their sample, while B was by far the most common haplogroup and C and D were also present in small numbers. This seems to clearly rule out one theory about the Fremont, which is that they were composed in part of Athabascans on their way south from the Subarctic, and also casts in serious doubt other theories linking them to later cultures on the Plains (where haplogroup A is also very common). It’s true that there is internal cultural variation within the construct “Fremont” and it’s quite possible there was genetic variation as well, but the Great Salt Lake Fremont were the furthest north of the identified subdivisions and the closest to the Plains, so if even they show more genetic similarities to the Southwest that is strong evidence against theories associating them with areas to the north and east.

It’s also noteworthy that the Fremont distribution is in contrast to what Lorenz and Smith found among modern Numic peoples who now occupy the Fremont’s Great Basin home. The Numic Paiute/Shoshone sample that Lorenz and Smith looked at lacked haplogroup A, but it showed a very high proportion of haplogroup D (the highest in their whole study, in fact) and a low proportion of B and C. This doesn’t totally rule out some Fremont contribution to Numic ancestry, but it makes it seem unlikely that there was substantial genetic continuity between Fremont and Numic populations, which supports the “Numic Expansion” hypothesis for the late prehistory of the Great Basin. Smith and his student Frederika Kaestle later published a paper making this exact argument, using not only the Fremont data but additional ancient remains from the western Great Basin to argue that the differences in haplogroup frequencies supported a replacement of the earlier Basin inhabitants by the Numa.

Following up on this research, a subsequent paper by the same Utah researchers added in data from the Anasazi. They successfully assigned 27 Anasazi samples to haplogroups. Of these, 12 were from southeastern Utah, 9 were from Canyon del Muerto, 4 were from Canyon de Chelly, and 2 were from Chaco Canyon. Of the Chaco remains, one came from the debris in Room 56 at Pueblo Bonito, a part of the north burial cluster in Old Bonito which was very crudely worked over by Warren K. Moorehead in the 1890s. The other I can’t seem to find any specific information on. All of the Anasazi remains analyzed in this study were from the collections of the American Museum of Natural History, which makes me surprised that only two Chaco samples were involved. It’s possible that more were analyzed but only these two produced enough DNA to work with. In any case, if in fact there are more Chaco remains at the AMNH that have not yet been analyzed for DNA it would be very helpful to analyze them.

The results of this analysis were consistent with the standard archaeological understanding that the modern Pueblos are the descendants of the Anasazi. B was the most common haplogroup, with smaller levels of A and C. D wasn’t present at all, and two of the specimens didn’t fall into any of the four haplogroups, implying that they might have belonged to X. (The two Chaco samples belonged to haplogroups B and C; the sample from Room 56 belonged to haplogroup B.) Note that A is present here in populations dating well before any likely admixture with Athabascans, which is evidence against Lorenz and Smith’s contention that the presence of A in modern Pueblos can be attributed entirely to mixture with Athabascans.

Based on the dominance of B and low levels of other haplogroups, these researchers concluded that the Anasazi remains they analyzed were not significantly different from the Fremont remains they had analyzed earlier, adding further support to their contention that the Fremont pattern with the Pueblos. Note, however, that the Fremont hadn’t shown haplogroup A at all, while the Anasazi had it at a low but still respectable level (22%). Also, the Fremont showed a low level of haplogroup D, which the Anasazi didn’t have at all. These differences don’t necessarily mean the Fremont and Anasazi weren’t related, of course, but they do show how much that similarity is a judgment call supported by questionable statistics. In this case one big problem with the statistical analysis was treating the haplogroup frequencies as ratio-level data, which implies that they are meaningfully representative of the underlying populations despite the very small and non-random samples. This is highly implausible. This problem means that the authors’ conclusions about whether differences between samples were “significant” or not in a statistical sense is not really meaningful since it can’t reasonably be expected to generalize to the populations, which are what we really care about.

In addition, as Connie Mulligan pointed out in the general paper on aDNA that I discussed previously, the differences that the Davis researchers found between the haplogroup frequencies of the Fremont and Numic samples, which they used as evidence of a lack of population continuity, were actually quite similar statistically to the differences the Utah researchers found between the Fremont and Anasazi, which they interpreted as not being significant! This disconnect goes to show that there’s actually quite a bit of subjective judgment in interpreting results like this, despite the superficial impression of “objective” statistical data.

One way to overcome this confusion would be to increase the number of samples analyzed and try to make them as close to representative of the underlying populations as possible. That would certainly help, but the fundamental problem of defining the ancient population of interest, and the apparent impossibility of analyzing a sample from it that could be assumed to be truly representative, are daunting challenges. A more productive approach, which subsequent research has in fact been following, is to do more in-depth analysis of available samples, so that more detailed data than crude haplogroup assignments are possible.

One way to do more in-depth analysis would be to move away from relying exclusively on haplogroup assignments and look instead at the nuclear genome. Sequencing the whole nuclear genome provides vastly more, and more statistically robust, information than mitochondrial haplogroup assignment, as commenter ohwilleke pointed out in response to my initial DNA post. Most of the studies mentioned in my previous post in other parts of the world have used this methodology, with very informative results. This type of analysis has, however, not been done on ancient remains from the American Southwest to my knowledge. I’m not sure why exactly, but there are various reasons including cost and level of preservation of remains that could account for this lacuna.

Instead, Southwestern researchers have mostly doubled down on mitochondrial haplotype analysis and extended its reach by looking at further mutations within the defined haplogroups to identify sub-haplogroups that can further narrow down genetic relationships. This has been a productive line of investigation, as exemplified by a very interesting paper from 2010 dealing with Chaco-era sites in the area of Farmington, New Mexico.

B-Square Ranch, Farmington, New Mexico

The paper, by Meradeth Snow and David Glenn Smith of Davis and Kathy Durand of Eastern New Mexico University, analyzed human remains from two sites on the B-Square Ranch, a large ranch that includes most of the land south of the San Juan River in Farmington. The ranch is owned by the Bolack family, which has long been prominent in local and statewide affairs. Its patriarch for many years was Tom Bolack, who was governor of New Mexico for a brief period in the 1960s and was also well known for his elaborate produce displays at the State Fair. His son Tommy Bolack, who took over management of the ranch when Tom died, has long had an interest in archaeology and did his own excavations in various of the many archaeological sites on the ranch. In recent years rather than continuing his own excavations he has worked with Linda Wheelbarger, a professional archaeologist who teaches at San Juan College in Farmington, to conduct field schools in the summers for SJC students as well as analyses of artifacts and human remains from both these recent excavations and his own earlier amateur work.

Among these analyses was the aDNA analysis of remains that Bolack excavated from the Tommy and Mine Canyon sites, two small-house sites on the ranch dating to the Chaco era. The Tommy site is slightly earlier, dating to approximately AD 800 to 1100, while the Mine Canyon site dates to approximately AD 1100 to 1300. Since the Tommy site seems to have been abandoned at approximately the same time the Mine Canyon site was founded, one obvious interpretation is that the Mine Canyon site was founded by the same people who had previously lived at the Tommy site. The DNA evidence, however, challenges this interpretation and suggests a more complicated story.

For this study, 73 samples were sent to Davis for aDNA analysis. This included a mix of tooth and bone samples. Of these samples, 48 (65.7%) could be assigned to a mitochondrial haplogroup. Of these, 26 were from the Tommy site and 12 from the Mine Canyon site.

The successfully analyzed samples from the Tommy site showed a typical distribution of haplogroups for a Southwestern population: 3% A, 69% B, 14% C, and 14% D. (This study didn’t look for haplogroup X, and all successfully analyzed samples fell into one of the other founding haplogroups.) The Mine Canyon sample, however, showed a very unusual distribution: 58% A, 33% B, 8% C, and 0% D. This is an exceptionally high proportion of haplogroup A, which is generally fairly rare in the Southwest except in Athabascan groups which are generally thought to have arrived in the region well after these sites were abandoned. Haplogroup A is also very common in Mesoamerica, which makes its dominance in a Chaco-associated site particularly intriguing given the evidence for contact with Mexico seen at Chaco Canyon itself and some outlying Chacoan sites.

The authors are careful to note that these are very small sample sizes, which makes sampling bias a very real possibility to account for this sort of striking result. They compare these distributions to several other ancient and modern Southwestern and Mesoamerican populations using Fisher’s exact test and find, unsurprisingly, that the Tommy site sample isn’t significantly different from other ancient Southwestern populations but is significantly different from all the modern populations as well as the ancient Mesoamerican ones. The Mine Canyon sample, on the other hand, was found to be significantly different from all the ancient Southwestern samples as well as all the modern Southwestern ones except the Athabascan Navajo and Apache, while it wasn’t significantly different from any of the ancient or modern Mesoamerican samples. This result is clearly driven primarily by the unusually high proportion of haplogroup A at Mine Canyon, which means it doesn’t really add much to the paper. Although Fisher’s exact test does take into account the small sample sizes, it doesn’t address the more fundamental problem with this sort of use of statistics on this type of data which can’t really be trusted to be representative of the underlying population of interest. This is the sort of thing I was talking about in the earlier post under the somewhat tongue-in-cheek label of “elaborate statistical techniques” on data that don’t necessarily fit the necessary requirements for their use. This sort of technique is not actually very elaborate compared to more sophisticated statistical analyses used for studies of whole genomes, where the number of data points is immense and they can actually be assumed to be representative of the analyzed individual’s full ancestry. Calculating P-values for differences between two samples based on four data points for each, when neither sample is necessarily representative of its underlying population of interest, is not very useful, but very common in mtDNA studies at least in the Southwest. To their credit, the authors of this paper are well aware of the weaknesses of this part of it and are careful to downplay the significance of the statistical analysis.

With these intriguing preliminary results, the researchers attempted further sequencing to identify more specific mutations that might define sub-haplogroups and clarify relationships on a more granular scale. Of the 48 samples that could be assigned to haplogroups, 23 were successfully sequenced for mutations in a region of the mitochondrial genome known to be highly variable. (Note how small the sample gets with subsequent levels of analysis.) Poor preservation was a major problem at this point, and there wasn’t enough genetic material remaining to construct the sort of network diagram that is often included in papers like this, showing specific mutations and the relationships they imply between specific ancient and modern samples.

The most interesting results from this further sequencing were with haplogroup A. Of the 8 samples initially identified as belonging to this haplogroup, 6 samples from the Mine Canyon site showed two distinctive mutations that are otherwise known only from 3 modern Zuni samples, along with one Tohono O’odham and one Chumash sample. Importantly, this set of mutations is unknown from both Mesoamerican and Athabascan groups. This is strong evidence that the dominance of haplogroup A at the Mine Canyon site does not indicate either migration from Mesoamerica or an early Athabascan presence in the Southwest; instead, it seems that this site just happens to have had an unusually high proportion of a rare but natively Southwestern lineage which survived into modern times at Zuni (and may have had some connections further west). The samples belonging to haplogroup B similarly showed the dominance of a sub-haplogroup distinctive to the Southwest and unknown in Mesoamerica.

The differences between the Tommy site and the Mine Canyon site in haplogroup frequencies, while they may well be a function in part of the small sample sizes, may also provide evidence for complex population movements within the late prehistoric Southwest. The exact parameters of these movements can’t be defined until more evidence is available from other areas, however, especially Chaco Canyon and the Mesa Verde region.

Overall, despite the poor preservation of the samples involved, this study provides important support for a finding that has come out consistently across all lines of evidence relating ancient to modern Pueblo people: there is a lot of evidence for continuity over time on a regional scale with complex movements within the Southwest, but little to no evidence of significant population movement into or out of the Southwest in recent centuries. (There is a whole other debate about the extent of population movement into the Southwest much earlier, at the time when agriculture was first introduced, which I haven’t discussed much in these posts and which isn’t of much importance for the specific issue I’m addressing here.) I think there is a lot of potential for more detailed reconstruction of movement within the Southwest based on a combination of lines of evidence, but we’re certainly not there yet.

I’ve gotten some questions about how the DNA evidence relates to the issue of hierarchy at Chaco. I’ll have a more extensive post on the evidence for social hierarchy, which I think is extensive, but the short answer is that DNA doesn’t really provide any evidence one way or the other on this point. Since all evidence points to a general pattern of population continuity in the Southwest at least since the introduction of agriculture, the genetic patterns of any elites that arose wouldn’t be likely to differ in any noticeable way from those of the commoners they rose from. Indeed, the one sample to be analyzed for mitochondrial DNA that is very likely to come from an elite Chacoan context, the sample from Room 56 at Pueblo Bonito, belonged to haplogroup B, the most common in both ancient and modern Southwestern populations. It’s theoretically possible to imagine an elite group immigrating into the Southwest from Mesoamerica, and theories have been proposed along these lines, but the DNA evidence doesn’t particularly support this, and it’s much more likely based on all lines of evidence that the rise of an elite at Chaco was a primarily indigenous development involving some indirect influence from Mexico but little to no permanent population movement over that distance.

This is the last substantive post in my series about “tracing the connections” between the ancient and modern Southwest, although I will probably do a follow-up post linking to all the others for the convenience of readers. Overall, I think these posts have shown that we have substantial evidence from various perspectives that the modern Pueblos are the descendants of the ancient Anasazi (and other prehistoric Southwestern groups), but the evidence we have so far is not sufficient to connect any specific ancient sites with any specific modern pueblos. I am hopeful, however, that that may change as more evidence comes in and we are able to tie together new data with the evidence we already have to make some more specific connections.Carlyle SW, Parr RL, Hayes MG, & O’Rourke DH (2000). Context of maternal lineages in the Greater Southwest. American journal of physical anthropology, 113 (1), 85-101 PMID: 10954622

I’m still working on the follow-up to my DNA post, but in the meantime I’ve seen a few new reports of interesting research in other parts of the world using techniques similar to what I was talking about. This will provide some context for the Southwest-specific research I’ll discuss later, which is still at a much more rudimentary level that hasn’t yet produced such striking results.

First, commenter ohwilleke, in addition to leaving a long and informative comment about analytical techniques and the usefulness of full-genome sequencing as opposed to mitochondrial studies, points to a recent study of modern inhabitants of Rapanui (Easter Island) that shows clear evidence of prehistoric genetic mixture with people from South America. There have long been theories that there was contact between these populations, but this appears to confirm them with the most solid evidence yet, and provides another glimpse of the complexity of human history. (I’ll address the issue of full genomic sequencing, which has not yet been used on any ancient remains from the Southwest to my knowledge, in the follow-up post.)

Second, there have apparently been two new articles (only one of which I could find, since the news story doesn’t even give the title of the journal the other one was published in) using aDNA techniques on ancient remains from Europe. One study, by a large team including David Reich of Harvard Medical School, found three major sources of ancestry for ancient Europeans: early hunter-gatherers, presumably of African origin; early farmers of Near Eastern origin (which seems to strongly support theories that the spread of agriculture across Europe had migration of people as an important component) who apparently interbred with the hunter-gatherer population to some extent; and a previously unknown group with links to Central Asia and possibly associated with the introduction of Bronze Age material culture. The second study, which looked at remains from later dates than the first, appears to have also found a fourth group that entered eastern Europe during the Iron Age.

Finally, reaching back to a much earlier date, a bone found in a riverbank in Siberia yielded the oldest human genome sequenced to date. Radiocarbon-dated to between 43,000 and 47,000 years ago, the genome is particularly noteworthy because it contains a higher proportion of segments of Neanderthal origin than modern human genomes, which apparently has important implications for theories about the initial peopling of the world by modern humans.

Now, I don’t have access to any of these papers so I haven’t read any of them myself. My comments about them are based on the abstracts and the coverage they’ve gotten in the media, which is of course notoriously unreliable when it comes to highly technical subjects. Still, this should give a sense of the kinds of topics DNA studies are weighing in on. As I said before, DNA research in the Southwest is still at a much more rudimentary level, so don’t expect to see this kind of thing any time soon. It is developing, though, and has great potential to answer important questions of archaeological interest. I’ll explain more about the work that has been done in the next post.

To wrap up my series on tracing the connections between ancient Pueblo sites like Chaco Canyon and the modern Pueblos, I’d like to discuss a type of evidence I haven’t discussed much but that people often ask about: DNA evidence. This is the most direct way to tie one population to another, at least in theory, but it’s actually quite difficult to draw any specific conclusions from the work that has been done so far, and that’s not necessarily going to improve as more research is done. Which is not to say that research along these lines has been worthless; it hasn’t revealed anything inconsistent with data from other sources so far, but that in itself is interesting and provides support for the other approaches that have been tried. Because this is such a huge and important topic, I’ve decided to break my discussion of it into two posts, one on the archaeological study of DNA in general, and another on the application of these techniques to the Southwest in particular.

There are many different types of DNA analyses that can in theory be done, but when it comes to archaeological questions, especially those involving connections between ancient sites and modern people, it is generally necessary to analyze remains excavated by archaeologists. This involves studying what is known as “ancient DNA” (or “aDNA” for short), in addition to the DNA of modern populations. As Connie Mulligan of the University of Florida noted in an article published in American Antiquity in 2006, aDNA studies have a lot of potential but also a lot of challenges. Some of the major issues involved in aDNA research are preservation of the DNA, without which any study has no chance of success, and interpretation of the results of a successful analysis of ancient material.

Because DNA, like any other organic material, decays over time, aDNA studies are more difficult and expensive than DNA studies of modern populations, and in some cases there is simply not enough DNA left in archaeological material to do any analysis at all. Preservation is a function, in part, of local environmental conditions, which in the arid Southwest tend to be favorable for preserving organic material, so this is less of a concern in this area than in many others.

Another major consideration in doing aDNA analysis is contamination. The technique that makes aDNA analysis possible is called Polymerase Chain Reaction (PCR), which involves taking a small amount of DNA and exposing it to a chemical reaction that creates billions of copies which can then be analyzed. This can be enormously useful, but the reaction is very sensitive and if any extraneous organic material is introduced it is likely to reproduce its DNA instead of the ancient DNA, which can totally destroy the validity of the analysis. The main concern with aDNA analyses of human remains is modern human DNA from the researchers themselves, and this has been an issue with many studies. These days the major laboratories that do aDNA analysis have elaborate procedures to ensure that modern human DNA doesn’t contaminate their samples, and these are typically spelled out in the papers resulting from this research.

Furthermore, as Mulligan discusses, it’s important that researchers have a clear sense of what questions they are asking and how successful aDNA analyses are likely to be in answering them. For example, DNA analysis is unlikely to be able to unambiguously identify a given set of ancient remains as belonging (or ancestral) to a specific tribal group, since genetic affiliation doesn’t correlate with cultural identity at anything close to that level of specificity. In other words, aDNA analysis can potentially identify remains as being of Native American rather than European origin, but it can’t unambiguously identify remains with any particular modern tribe. On the other hand, it is potentially possible to use aDNA studies to identify migrations and population replacement in the past, if the groups in question are sufficiently distinct genetically. Mulligan actually uses an example from the prehistoric Southwest, which I’ll discuss further in the next post, to illustrate how it can be tricky to interpret differences in genetic characteristics between populations, especially at the level of detail at which these analyses are often conducted.

These concerns aside, DNA analysis can certainly be a powerful tool for understanding the past, especially when aDNA studies can be integrated with studies of modern DNA. A great example of this is a study that was recently published in Science about the prehistory of the North American Arctic. In this paper, which is available free on the Science website, the researchers report on a combination of aDNA and modern DNA analyses that demonstrate clearly that the people of the mysterious Dorset culture that inhabited Arctic Canada and Greenland from about 800 BC to AD 1300 are not ancestral to the modern Inuit inhabiting the same area, who are instead descended from the people of the Thule culture who immigrated into Canada from northern Alaska around AD 1200. This is solid, careful research that shows what DNA studies can reveal about the human past.

Much of the aDNA research in the Americas has focused on mitochondrial DNA (mtDNA), which is contained in the mitochondria of each cell, as opposed to nuclear DNA, which is contained in the cell nucleus. There are two main reasons for this.

One is that mitochondrial DNA is passed on (generally) unchanged through the maternal line, as opposed to nuclear DNA which undergoes meiosis, the process by which DNA from the mother and father is recombined in the course of creating a new embryo, meaning that any part of the genome that has gone through it cannot be easily traced from generation to generation. Mitochondrial DNA, in contrast, is passed on directly from mother to child, and the only changes are whatever mutations develop over time, which can be used to define specific haplogroups, or genetic groupings sharing certain distinctive mutations that are interpreted as indicating shared descent. Within each haplogroup, further mutations can be used to define various sub-haplogroups, which indicate closer relationship among the haplotypes (individual genetic profiles) that comprise them. The Y chromosome, which is passed on directly from father to son, isn’t affected by recombination during meiosis and can be used to trace descent in a similar fashion. However, mtDNA is more widely used for aDNA studies than Y-chromosome DNA, due to an additional difference between mtDNA and nuclear DNA. Due to the structure of mitochondria, each cell contains many more copies of its mtDNA than of its nuclear DNA, so mtDNA is much more likely to survive in ancient samples than nuclear DNA. This means there is much greater probability that studies of mtDNA using PCR will identify DNA to be replicated, and the result is that the existing database of mtDNA available for statistical analysis is much larger than that for nuclear DNA, including Y-chromosome DNA. Most aDNA studies in North America, at least, have therefore used mtDNA as a primary focus for research.

Early research on both ancient and modern DNA identified four main mitochondrial haplogroups among Native American populations. These were labeled A, B, C, and D. (Haplogroups are conventionally identified by capital letters, with more specific sub-haplogroups indicated by sequences of numbers and lowercase letters following the haplogroup letter.) These haplogroups all arose from earlier East Asian haplogroups, which agrees with the traditional interpretation that Native Americans descend from Asian groups that migrated across the Bering Strait. Some modern populations in these early studies showed low levels of an additional haplogroup, X, which had previously only been documented in Europeans. There was some question at first about whether this indicated post-Contact admixture with Europeans or an additional “founding” haplogroup, but it was later found in aDNA, showing clearly that it was indeed ancient in the Americas. The implications of this finding are hard to understand, but the general consensus at this point seems to be that the American examples descend from a very ancient and otherwise unknown Central Asian offshoot of the European X haplogroup. Wherever it came from, however, it is now quite clear that X is one of the founding haplogroups in the Americas.

Much aDNA research in North America, then, has focused on identifying the haplogroups of ancient remains and comparing them to those of other populations, both ancient and modern. Much of this research has involved treating assemblages of ancient remains (either from single sites or across a whole archaeological “culture”) as samples that can be compared statistically to samples from modern tribes. I find this dubious, since the ancient samples are typically small and there’s no way to tell how representative they are of the actual underlying population (however it’s defined). The statistical procedures often used to analyze haplogroup frequencies implicitly assume that these are random samples representative of the population, but there’s no real way to know if this is true and in most cases no particular reason to think it is. In theory it’s possible that the modern samples, at least, are representative of their populations, but I suspect it’s often not the case in practice here either. For both modern and ancient samples, it’s likely that other factors, such as level of preservation and willingness to provide samples, have strongly affected the composition of the samples. These factors may or may not have skewed the representativeness of the samples; the point is that there’s no real way to tell.

Given this sampling issue, I think the most conservative and defensible approach is to treat haplogroup distributions as nominal-level data: the most we can really say about a given haplogroup in a given sample is whether it is present or absent. That’s not very helpful, though, and it may be reasonable to take a further leap and treat the distributions as ordinal-level data: this allows us to make use of the fact that some haplogroups are much more common in a given sample than others to make some broad conclusions about haplogroup distributions on a larger scale. What isn’t justified, however, is treating the frequencies of haplogroups in a sample as interval/ratio-level data: using the actual numbers as if they are meaningfully representative of the underlying population, and plugging them into elaborate statistical formulas to compare them to other samples/populations. Not all aDNA studies do this sort of thing, but it’s common enough that I think it’s important to emphasize that it’s a problematic approach at best, and that any conclusions regarding probable relationships between populations based on this method shouldn’t be taken very seriously.

A better way to go beyond the crude data of haplogroup assignment is to sequence additional portions of the mitochondrial genome that are known to contain mutations that define sub-haplogroups within the assigned overall haplogroup. Enough research has been done at this point that quite a few sub-haplogroups are known, and when they show up in multiple samples, either ancient or modern, that provides a much firmer basis for hypothesizing meaningfully close relationships than statistical comparisons of haplogroup distributions among whole samples. Furthermore, since the mutations that define sub-haplogroups can be grouped hierarchically, it’s possible to construct trees showing how individuals in a given sample, or even across samples, that belong to the same haplogroup relate to each other. (Note that this isn’t quite the same as showing how the people were actually related, since we don’t know when the mutations that define these groups actually occurred or how the people whose remains were sampled were related to the people in whom the mutations originally occurred.) There’s a probabilistic aspect to this type of evidence, since there are multiple ways a particular set of mutations could have ended up together in the same haplotype, and determining the most likely sequence of events can require modeling and simulation. The more samples are analyzed, the larger the database of known mutations and sub-haplogroups becomes, and the more reliable the conclusions that can be drawn about relationships are.

So that’s the basic outline of how ancient DNA analysis works and the methodological concerns that need to be kept in mind when evaluating it. In the next post, we’ll look at some of the specific studies that have applied these methods to the Southwest, and what their results can and can’t tell us about Southwestern prehistory.Mulligan, C. (2006). Anthropological Applications of Ancient DNA: Problems and Prospects American Antiquity, 71 (2) DOI: 10.2307/40035909